Hi Dave,
Thanks for the help. That did indeed allow suppose.nab to compile.
And, I can get suppose to run on PDB files without chain IDs, e.g.,
ATOM 374 CA LYS 36 -22.830 4.600 -4.951 1.00 0.00
ATOM 375 HA LYS 36 -22.132 4.086 -4.304 1.00 0.00
ATOM 376 CB LYS 36 -22.534 6.120 -4.915 1.00 0.00
However, it seems to choke (bus error -- see below) on PDB files that look like this:
foster% head -5 ca.pdb
ATOM 1 N ARG A 7 21.584 8.339 6.922 1.00 95.61 N
ATOM 2 CA ARG A 7 22.934 8.080 7.501 1.00 95.63 C
ATOM 3 C ARG A 7 24.017 8.326 6.450 1.00 95.47 C
ATOM 4 O ARG A 7 24.000 7.716 5.380 1.00 95.54 O
ATOM 5 CB ARG A 7 23.004 6.640 8.045 1.00 96.00 C
foster% suppose -fit ::CA ca.pdb cb.pdb
addstrand: strand A already in mol
Molecule 1 = ca.pdb
addstrand: strand B already in mol
Molecule 2 = cb.pdb
Bus error
?
-M
On Dec 20, 2010, at 4:17 PM, case wrote:
> On Mon, Dec 20, 2010, Mark Foster wrote:
>>
>> I (finally) succeeded in installing AmberTools 1.4 on my OSX 10.6 mac
>> using fink-installed gcc-4.4. To do so, I replaced instances of gcc and
>> g++ in the configure script with gcc-4 and g++4. Most tests PASSED.
>
> If the tests pass, it means you can run NAB.
>
>>
>> However, I am not able to run NAB independently:
>>
>> [kex:AmberTools/examples/suppose] foster% nab --v
>
>> Undefined symbols:
>> "_main", referenced from:
>> start in crt1.10.5.o
>> ld: symbol(s) not found
>> collect2: ld returned 1 exit status
>> cc failed!
>
> This is expected...you tried to compile a (non-existent) NAB program.
> Admittedly, there should be a better error message if there is no input file.
>
>>
>> [kex:AmberTools/examples/suppose] foster% nab suppose.nab
>> Undefined symbols:
>> "_MAT_istrue", referenced from:
>> _main in ccFNRvC6.o
>
> Ah...this is a bug, undetected for a good many years! I will post a bugfix,
> but for now, edit $AMBERHOME/AmberTools/src/nss/Makefile, and remove line 25
> (" matop.o \"). Then cd to $AMBERHOME/AmberTools/src and type "make
> nabonly".
>
> Thanks for the report.
>
> ....dac
>
>
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-----------
Mark P. Foster, Ph.D.
Professor, Interim Chair Department of Biochemistry
(614) 292-1377 The Ohio State University
FAX 292-6773 484 West 12th Ave.
foster.281.osu.edu Columbus, OH 43210-1214
http://www.biosci.ohio-state.edu/~mfoster
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Received on Mon Dec 20 2010 - 14:00:03 PST
